casa-mp-base

# -*- coding: utf-8; mode: tcl; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:ft=tcl:et:sw=4:ts=4:sts=4

​

PortSystem              1.0

PortGroup               github 1.0

​

github.setup            BenLangmead bowtie 1.2.3 v

revision                0

categories              science biology

platforms               darwin

maintainers             {mcalhoun @MarcusCalhoun-Lopez} openmaintainer

license                 Artistic-1 LGPL-3+

​

description             an ultrafast, memory-efficient short read aligner

​

long_description        Bowtie is ${description}. It aligns short DNA sequences \

                        (reads) to the human genome at a rate of over 25 million \

                        35-bp reads per hour. Bowtie indexes the genome with a \

                        Burrows-Wheeler index to keep its memory footprint small: \

                        typically about 2.2 GB for the human genome (2.9 GB for \

                        paired-end).

​

homepage                http://bowtie-bio.sourceforge.net/

​

checksums               rmd160  a09f5d4dd685619ab60eef70b08c3b9d376bf85a \

                        sha256  9a62e7959a11aa2229722e20800441ce4ecbb2f9e74dd29bd5b2c6f6e4553db8 \

                        size    7894211

​

patchfiles-append       patch-Makefile.diff \

                        patch-seqan.diff

​

post-patch {

    reinplace -W ${worksrcpath} \

        "s|^#!/usr/bin/env python|#!${prefix}/bin/python2.7|" \

        bowtie \

        bowtie-build \

        bowtie-inspect

}

​

supported_archs         x86_64 ppc64

installs_libs           no

​

depends_build-append    port:seqan-1

​

depends_lib-append      port:zlib \

                        port:tbb

​

depends_run-append      port:python27

​

# replicate values from Makefile prior to patching

configure.optflags      -O3

configure.cppflags-prepend \

                        -I${prefix}/include/seqan-1

​

configure.cmd           printenv

configure.pre_args

configure.universal_args

configure.post_args     {>> Makefile.macports.inc}

​

destroot.args-append    prefix=${prefix}

​

post-destroot {

    xinstall -d ${destroot}${prefix}/share/doc/${name}

    xinstall -m 644 -W ${worksrcpath} \